# Transcript expression inference and differential expression analysis for RNA-seq data

## Documentation for package ‘BitSeq’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

BitSeq-package | Bayesian Inference of Transcripts from Sequencing data
BitSeq | Bayesian Inference of Transcripts from Sequencing data
estimateDE | Estimate condition mean expression and calculate Probability of Positive Log Ratio(PPLR)
estimateExpression | Estimate expression of transcripts
estimateExpressionLegacy | Estimate expression of transcripts
estimateHyperPar | Estimate hyperparameters for DE model using expression samples and joint mean expression
estimateVBExpression | Estimate expression of transcripts using VB
getDE | Estimate Probability of Positive Log Ratio
getExpression | Estimate transcript expression
getGeneExpression | Calculate gene expression or relative within gene expression
getMeanVariance | Calculate mean and variance of expression samples
getWithinGeneExpression | Calculate gene expression or relative within gene expression
loadSamples | Loading and saving expression samples
parseAlignment | Compute probabilities of alignments
tri.file.hasGeneNames | Manage file containing information about transcript reference
tri.file.setGeneNames | Manage file containing information about transcript reference
tri.hasGeneNames | Manage information about transcript reference
tri.load | Manage information about transcript reference
tri.save | Manage information about transcript reference
tri.setGeneNames | Manage information about transcript reference
writeSamples | Loading and saving expression samples